Soil aggregation is of great importance in agriculture due to its positive effect on soil physical properties, plant growth and the environment. A long-term (1996–2008) field experiment was performed to investigate the role of mycorrhizal inoculation and organic fertilizers on some of soil properties of Mediterranean soils (Typic Xerofluvent, Menzilat clay–loam soil). We applied a rotation with winter wheat (Triticum aestivum L.) and maize (Zea mays L.) as a second crop during the periods of 1996 and 2008. The study consisted of five experimental treatments; control, mineral fertilizer (300–60–150kgN–P–Kha⁻¹), manure at 25tha⁻¹, compost at 25tha⁻¹ and mycorrhiza-inoculated compost at 10tha⁻¹ with three replicates. The highest organic matter content both at 0–15cm and 15–30cm soil depths were obtained with manure application, whereas mineral fertilizer application had no effect on organic matter accumulation. Manure, compost and mycorrhizal inoculation+compost application had 69%, 32% and 24% higher organic matter contents at 0–30cm depth as compared to the control application. Organic applications had varying and important effects on aggregation indexes of soils. The greatest mean weight diameters (MWD) at 15–30cm depth were obtained with manure, mycorrhiza-inoculated compost and compost applications, respectively. The decline in organic matter content of soils in control plots lead disintegration of aggregates demonstrated on significantly lower MWD values. The compost application resulted in occurring the lowest bulk densities at 0–15 and 15–30cm soil depths, whereas the highest bulk density values were obtained with mineral fertilizer application. Measurements obtained in 2008 indicated that manure and compost applications did not cause any further increase in MWD at manure and compost receiving plots indicated reaching a steady state. However, compost with mycorrhizae application continued to significant increase (P<0.05) in MWD values of soils. Organic applications significantly lowered the soil bulk density and penetration resistance. The lowest penetration resistance (PR) at 0–50cm soil depth was obtained with mycorrhizal inoculated compost, and the highest PR was with control and mineral fertilizer applications. The results clearly revealed that mycorrhiza application along with organic fertilizers resulted in decreased bulk density and penetration resistance associated with an increase in organic matter and greater aggregate stability, indicated an improvement in soil structure.